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mSystems. 2019 Feb 5;4(1). pii: e00265-18. doi: 10.1128/mSystems.00265-18. eCollection 2019 Jan-Feb.

Bridging the Holistic-Reductionist Divide in Microbial Ecology.

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Department of Environmental Systems Science, ETH Zürich, Zürich, Switzerland.
Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland.
Department of Environmental Microbiology, EAWAG, Dübendorf, Switzerland.


Microbial communities are inherently complex systems. To address this complexity, microbial ecologists are developing new, more elaborate laboratory models at an ever-increasing pace. These model microbial communities and habitats have opened up the exploration of new territories that lie between the simplicity and controllability of "synthetic" systems and the convolution and complexity of natural environments. Here, we discuss this classic methodological divide, we propose a conceptual perspective that integrates new research developments, and we sketch a 3-point possible roadmap to cross the divide between controllability and complexity in microbial ecology.


metagenomics; microbial communities; microbial diversity; synthetic ecology

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